☰ Navigation Tabs
Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GVH pdb entry 3GVH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 JCSG+ SCREEN, H3: 25% PEG 3350, 100MM BISTRIS, BRABA.00005.A AT 28.5MG/ML, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.39 α = 90 b = 193.9 β = 90 c = 102.68 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2009-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.25 193.9 97.3 0.051 18.82 4.2 102350 99622 -3 28.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.31 83.7 0.152 5.6 2 7486
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT pdb entry 3GVH 2.25 193 99617 99617 5000 97.3 0.177 0.174 0.173 0.228 0.2237 RANDOM 14.95
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.49 0.67 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.254 r_dihedral_angle_4_deg 14.413 r_dihedral_angle_3_deg 14.105 r_dihedral_angle_1_deg 5.58 r_scangle_it 3.748 r_scbond_it 2.34 r_angle_refined_deg 1.525 r_mcangle_it 1.412 r_angle_other_deg 0.927 r_mcbond_it 0.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.254 r_dihedral_angle_4_deg 14.413 r_dihedral_angle_3_deg 14.105 r_dihedral_angle_1_deg 5.58 r_scangle_it 3.748 r_scbond_it 2.34 r_angle_refined_deg 1.525 r_mcangle_it 1.412 r_angle_other_deg 0.927 r_mcbond_it 0.756 r_mcbond_other 0.232 r_chiral_restr 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13710 Nucleic Acid Atoms Solvent Atoms 1311 Heterogen Atoms 162
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling